OK, seems like TITANIC would be more appropriate name for this GPU model
...
It's just a pity that the issues are here perhaps only Amber specific
however
if there is problem e.g. with cuFFT, many other computational packages
should have
similar problems ?
M.
Dne Wed, 19 Jun 2013 19:21:53 +0200 Scott Le Grand <varelse2005.gmail.com>
napsal/-a:
> I have fixed the GB weirdness (I think). But now I have found a new
> issue
> with IPS simulations where I can repro bad behavior in 5 minutes or less
> (either Shake or the Local Forces misfire somehow in a way I can't quite
> figure out).
>
> I'm pretty dependent on NVIDIA at this point.
>
> Scott
>
>
>
> On Wed, Jun 19, 2013 at 9:55 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> Hi Scott,
>> thanks for update ! Regarding "GB/Titan" issue it is perhaps still
>> in debugging phase too (like cuFFT/Titan problem) if I understood well.
>>
>> Best,
>>
>> Marek
>>
>>
>>
>>
>> Dne Wed, 19 Jun 2013 17:50:51 +0200 Scott Le Grand
>> <varelse2005.gmail.com>
>> napsal/-a:
>>
>> > Hey Marek,
>> > No updates per se. I had a theory about what was going on that
>> proved to
>> > be wrong after testing, but I'm still waiting on NVIDIA to report
>> > something
>> > beyond having reproed the problem.
>> >
>> > Really really really interested in GTX 780 data right now...
>> >
>> >
>> >
>> > On Wed, Jun 19, 2013 at 8:20 AM, Marek Maly <marek.maly.ujep.cz>
>> wrote:
>> >
>> >> Hi all,
>> >>
>> >> just a small update from my site.
>> >>
>> >> As I have yesterday obtained announcement that the CUDA 5.5 is
>> >> now available for public (not just for developers).
>> >>
>> >> I downloaded it from here:
>> >>
>> >> https://developer.nvidia.com/**cuda-pre-production<
>> https://developer.nvidia.com/cuda-pre-production>
>> >>
>> >> It is still "just" release candidate ( as all Amber/Titan club
>> members
>> >> perfectly know :)) ).
>> >>
>> >> So I installed this newest release and recompiled Amber cuda code.
>> >>
>> >> I was hoping that maybe there was "silently" incorporated some
>> >> improvement (e.g. in cuFFT) as the result e.g. of Scott's bug report.
>> >>
>> >> The results of my 100K tests are attached. It seems that comparing
>> to my
>> >> latest
>> >> tests with CUDA 5.5. release candidate from June 3rd (when it was
>> >> accessible just for CUDA developers in the form of *.run binary
>> >> installer)
>> >> there
>> >> is some slight improvement - e.g. my more stable TITAN was able to
>> >> finish
>> >> successfully
>> >> all the 100K tests including Cellulose twice. But there is still an
>> >> issue
>> >> with JAC NVE/NPT irreproducible results. On my "less stable" TITAN
>> the
>> >> results are slightly better
>> >> then those older ones as well but still not err free (JAC/CELLULOSE)
>> -
>> >> see
>> >> attached file.
>> >>
>> >> FACTOR IX NVE/NPT finished again with 100% reproducibility on both
>> GPUs
>> >> as
>> >> usually.
>> >>
>> >> Scott, do you have any update regarding the "cuFFT"/TITAN issue which
>> >> you
>> >> reported/described
>> >> to NVIDIA guys ? The latest info from you regarding this story was,
>> that
>> >> they were able to
>> >> reproduce the "cuFFT"/TITAN error as well. Do you have any more
>> recent
>> >> information ? How long
>> >> time it might take to NVIDIA developers to fully solve such problem
>> in
>> >> your opinion ?
>> >>
>> >> Another thing. It seems that you successfully solved the "GB/TITAN"
>> >> problem in case of bigger molecular systems, here is your relevant
>> >> message
>> >> form June 7th.
>> >>
>> >> ------------------------------**----------------
>> >>
>> >> Really really interesting...
>> >>
>> >> I seem to have found a fix for the GB issues on my Titan - not so
>> >> surprisingly, it's the same fix as on GTX4xx/GTX5xx...
>> >>
>> >> But this doesn't yet explain the weirdness with cuFFT so we're not
>> done
>> >> here yet...
>> >> ------------------------------**---------------
>> >>
>> >> It was already after the latest Amber12 bugfix18 was released and
>> there
>> >> was no additional
>> >> bugfix released from that moment. So the "GB/TITAN" patch will be
>> >> released later maybe as the part of some bigger bugfix ? Or you
>> simply
>> >> additionally included it into bugfix 18 after it's release ?
>> >>
>> >>
>> >> My last question maybe deserves the new separate thread, but anyway
>> >> would
>> >> be interesting
>> >> to have some information how "Amber-stable" are GTX780 comparing to
>> >> TITANS
>> >> (of course based
>> >> on experience of more users or on testing more than 1 or 2 GTX780
>> GPUs).
>> >>
>> >> Best wishes,
>> >>
>> >> Marek
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Dne Mon, 03 Jun 2013 01:57:36 +0200 Marek Maly <marek.maly.ujep.cz>
>> >> napsal/-a:
>> >>
>> >>
>> >> Hi here are my results with CUDA 5.5
>> >>> (Total energy at step 100K(PME)/1000K(GB) (driver 319.23, Amber12
>> >>> bugfix
>> >>> 18 applied, cuda 5.5))
>> >>>
>> >>>
>> >>> No significant differences comparing the previous test with CUDA 5.0
>> >>> (I also added those data to the attached table with CUDA 5.5 test).
>> >>>
>> >>> Still the same trend instability in JAC tests, perfect stability and
>> >>> reproducibility
>> >>> in FACTOR_IX tests (interesting isn't it ? especially if we consider
>> >>> 23K
>> >>> atoms
>> >>> in JAC case and 90K atoms in case of FACTOR_IX). Again the same
>> >>> crashes in
>> >>> CELLULOSE
>> >>> test now also in case of TITAN_1. Also in stable and reproducible
>> >>> FACTOR_IX slightly
>> >>> changed the final energy values comparing to CUDA 5.0 case.
>> >>>
>> >>> GB simulations (1M steps) again perfectly stable and reproducible.
>> >>>
>> >>> So to conclude, Scott we trust you :)) !
>> >>>
>> >>> If you have any idea what to try else (except GPU bios editing,
>> perhaps
>> >>> too
>> >>> premature step at this moment) let me know. I got just last idea,
>> >>> which could be perhaps to try change rand seed and see if it has any
>> >>> influence in actual trends (e.g. JAC versus FACTOR_IX).
>> >>>
>> >>> TO ET : I am curious about your test in single GPU configuration.
>> >>> Regarding
>> >>> to your Win tests, in my opinion it is just wasting of time. They
>> >>> perhaps
>> >>> tells
>> >>> you just something about the GPU performance not about the eventual
>> GPU
>> >>> "soft" errs.
>> >>>
>> >>> If intensive memtestG80 and/or cuda_memtest results were negative
>> >>> there is
>> >>> in my opinion
>> >>> very unlikely that Win performace testers will find any errs, but I
>> am
>> >>> not
>> >>> an expert
>> >>> here ...
>> >>>
>> >>> Anyway If you learn which tests the ebuyer is using to confirm GPU
>> >>> errs,
>> >>> let us know.
>> >>>
>> >>> M.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Dne Sun, 02 Jun 2013 19:22:54 +0200 Marek Maly <marek.maly.ujep.cz>
>> >>> napsal/-a:
>> >>>
>> >>> Hi so I finally succeeded to compile GPU Amber part under CUDA 5.5
>> >>>> (after "hacking" of the configure2 file) with common results in
>> >>>> consequent tests:
>> >>>>
>> >>>> ------
>> >>>> 80 file comparisons passed
>> >>>> 9 file comparisons failed
>> >>>> 0 tests experienced errors
>> >>>> ------
>> >>>>
>> >>>> So now I am running the 100K(PME)/1000K(GB) repetitive benchmark
>> tests
>> >>>> under
>> >>>> this configuration: drv. 319.23, CUDA 5.5. , bugfix 18 installed
>> >>>>
>> >>>> When I finish it I will report results here.
>> >>>>
>> >>>> M.
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> Dne Sun, 02 Jun 2013 18:44:23 +0200 Marek Maly <marek.maly.ujep.cz>
>> >>>> napsal/-a:
>> >>>>
>> >>>> Hi Scott thanks for the update !
>> >>>>>
>> >>>>> Anyway any explanation regarding "cuFFT hypothesis" why there are
>> no
>> >>>>> problems
>> >>>>> with GTX 580, GTX 680 or even K20c ???
>> >>>>>
>> >>>>>
>> >>>>> meanwhile I also tried to recompile GPU part of Amber with
>> >>>>> cuda 5.5 installed before, I have obtained these errs
>> >>>>> already in configure phase:
>> >>>>>
>> >>>>> --------
>> >>>>> [root.dyn-138-272 amber12]# ./configure -cuda -noX11 gnu
>> >>>>> Checking for updates...
>> >>>>> Checking for available patches online. This may take a few
>> seconds...
>> >>>>>
>> >>>>> Available AmberTools 13 patches:
>> >>>>>
>> >>>>> No patches available
>> >>>>>
>> >>>>> Available Amber 12 patches:
>> >>>>>
>> >>>>> No patches available
>> >>>>> Searching for python2... Found python2.6: /usr/bin/python2.6
>> >>>>> Error: Unsupported CUDA version 5.5 detected.
>> >>>>> AMBER requires CUDA version == 4.2 .or. 5.0
>> >>>>> Configure failed due to the errors above!
>> >>>>> ---------
>> >>>>>
>> >>>>> so it seems that Amber is possible to compile only with CUDA 4.2
>> or
>> >>>>> 5.0
>> >>>>> at
>> >>>>> the moment:
>> >>>>>
>> >>>>> and this part of configure2 file has to be edited:
>> >>>>>
>> >>>>>
>> >>>>> -----------
>> >>>>> nvcc="$CUDA_HOME/bin/nvcc"
>> >>>>> sm35flags='-gencode arch=compute_35,code=sm_35'
>> >>>>> sm30flags='-gencode arch=compute_30,code=sm_30'
>> >>>>> sm20flags='-gencode arch=compute_20,code=sm_20'
>> >>>>> sm13flags='-gencode arch=compute_13,code=sm_13'
>> >>>>> nvccflags="$sm13flags $sm20flags"
>> >>>>> cudaversion=`$nvcc --version | grep 'release' | cut -d' '
>> -f5 |
>> >>>>> cut
>> >>>>> -d',' -f1`
>> >>>>> if [ "$cudaversion" == "5.0" ]; then
>> >>>>> echo "CUDA Version $cudaversion detected"
>> >>>>> nvccflags="$nvccflags $sm30flags $sm35flags"
>> >>>>> elif [ "$cudaversion" == "4.2" ]; then
>> >>>>> echo "CUDA Version $cudaversion detected"
>> >>>>> nvccflags="$nvccflags $sm30flags"
>> >>>>> else
>> >>>>> echo "Error: Unsupported CUDA version $cudaversion
>> detected."
>> >>>>> echo "AMBER requires CUDA version == 4.2 .or. 5.0"
>> >>>>> exit 1
>> >>>>> fi
>> >>>>> nvcc="$nvcc $nvccflags"
>> >>>>>
>> >>>>> fi
>> >>>>>
>> >>>>> -----------
>> >>>>>
>> >>>>> would it be just OK to change
>> >>>>> "if [ "$cudaversion" == "5.0" ]; then"
>> >>>>>
>> >>>>> to
>> >>>>>
>> >>>>> "if [ "$cudaversion" == "5.5" ]; then"
>> >>>>>
>> >>>>>
>> >>>>> or some more flags etc. should be defined here to proceed
>> >>>>> successfully ?
>> >>>>>
>> >>>>>
>> >>>>> BTW it seems Scott, that you are on the way to isolate the problem
>> >>>>> soon
>> >>>>> so maybe it's better to wait and not to loose time with cuda 5.5
>> >>>>> experiments.
>> >>>>>
>> >>>>> I just thought that cuda 5.5 might be more "friendly" to Titans
>> :))
>> >>>>> e.g.
>> >>>>> in terms of cuFFT function ....
>> >>>>>
>> >>>>>
>> >>>>> I will keep fingers crossed :))
>> >>>>>
>> >>>>> M.
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> Dne Sun, 02 Jun 2013 18:33:52 +0200 Scott Le Grand
>> >>>>> <varelse2005.gmail.com>
>> >>>>> napsal/-a:
>> >>>>>
>> >>>>> PS this *might* indicate a software bug in cuFFT, but it needs
>> more
>> >>>>>> characterization... And things are going to get a little stream
>> of
>> >>>>>> consciousness from here because you're getting unfiltered raw
>> data,
>> >>>>>> so
>> >>>>>> please don't draw any conclusions towards anything yet - I'm just
>> >>>>>> letting
>> >>>>>> you guys know what I'm finding out as I find it...
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> On Sun, Jun 2, 2013 at 9:31 AM, Scott Le Grand
>> >>>>>> <varelse2005.gmail.com>wrote:
>> >>>>>>
>> >>>>>> And bingo...
>> >>>>>>>
>> >>>>>>> At the very least, the reciprocal sum is intermittently
>> >>>>>>> inconsistent...
>> >>>>>>> This explains the irreproducible behavior...
>> >>>>>>>
>> >>>>>>> And here's the level of inconsistency:
>> >>>>>>> 31989.38940628897399 vs
>> >>>>>>> 31989.39168370794505
>> >>>>>>>
>> >>>>>>> That's error at the level of 1e-7 or a somehow missed
>> >>>>>>> single-precision
>> >>>>>>> transaction somewhere...
>> >>>>>>>
>> >>>>>>> The next question is figuring out why... This may or may not
>> >>>>>>> ultimately
>> >>>>>>> explain the crashes you guys are also seeing...
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> On Sun, Jun 2, 2013 at 9:07 AM, Scott Le Grand
>> >>>>>>> <varelse2005.gmail.com>wrote:
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>> Observations:
>> >>>>>>>> 1. The degree to which the reproducibility is broken *does*
>> >>>>>>>> appear to
>> >>>>>>>> vary between individual Titan GPUs. One of my Titans breaks
>> >>>>>>>> within
>> >>>>>>>> 10K
>> >>>>>>>> steps on cellulose, the other one made it to 100K steps twice
>> >>>>>>>> without
>> >>>>>>>> doing
>> >>>>>>>> so leading me to believe it could be trusted (until yesterday
>> >>>>>>>> where I
>> >>>>>>>> now
>> >>>>>>>> see it dies between 50K and 100K steps most of the time).
>> >>>>>>>>
>> >>>>>>>> 2. GB hasn't broken (yet). So could you run myoglobin for 500K
>> >>>>>>>> and
>> >>>>>>>> TRPcage for 1,000,000 steps and let's see if that's universal.
>> >>>>>>>>
>> >>>>>>>> 3. Turning on double-precision mode makes my Titan crash rather
>> >>>>>>>> than
>> >>>>>>>> run
>> >>>>>>>> irreproducibly, sigh...
>> >>>>>>>>
>> >>>>>>>> So whatever is going on is triggered by something in PME but
>> not
>> >>>>>>>> GB.
>> >>>>>>>> So
>> >>>>>>>> that's either the radix sort, the FFT, the Ewald grid
>> >>>>>>>> interpolation,
>> >>>>>>>> or the
>> >>>>>>>> neighbor list code. Fixing this involves isolating this and
>> >>>>>>>> figuring
>> >>>>>>>> out
>> >>>>>>>> what exactly goes haywire. It could *still* be software at
>> some
>> >>>>>>>> very
>> >>>>>>>> small
>> >>>>>>>> probability but the combination of both 680 and K20c with ECC
>> off
>> >>>>>>>> running
>> >>>>>>>> reliably is really pointing towards the Titans just being
>> clocked
>> >>>>>>>> too
>> >>>>>>>> fast.
>> >>>>>>>>
>> >>>>>>>> So how long with this take? Asking people how long it takes to
>> >>>>>>>> fix a
>> >>>>>>>> bug
>> >>>>>>>> never really works out well. That said, I found the 480 bug
>> >>>>>>>> within a
>> >>>>>>>> week
>> >>>>>>>> and my usual turnaround for a bug with a solid repro is <24
>> hours.
>> >>>>>>>>
>> >>>>>>>> Scott
>> >>>>>>>>
>> >>>>>>>> On Sun, Jun 2, 2013 at 7:58 AM, Marek Maly <marek.maly.ujep.cz>
>> >>>>>>>> wrote:
>> >>>>>>>>
>> >>>>>>>> Hi all,
>> >>>>>>>>>
>> >>>>>>>>> here are my results after bugfix 18 application (see
>> attachment).
>> >>>>>>>>>
>> >>>>>>>>> In principle I don't see any "drastical" changes.
>> >>>>>>>>>
>> >>>>>>>>> FACTOR_IX still perfectly stable/reproducible on both cards,
>> >>>>>>>>>
>> >>>>>>>>> JAC tests - problems with finishing AND/OR reproducibility the
>> >>>>>>>>> same CELLULOSE_NVE although here it seems that my TITAN_1
>> >>>>>>>>> has no problems with this test (but the same same trend I saw
>> >>>>>>>>> also
>> >>>>>>>>> before bugfix 18 - see my older 500K steps test).
>> >>>>>>>>>
>> >>>>>>>>> But anyway bugfix 18 brought here one change.
>> >>>>>>>>>
>> >>>>>>>>> The err
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> #1 ERR writtent in mdout:
>> >>>>>>>>> ------
>> >>>>>>>>> | ERROR: max pairlist cutoff must be less than unit cell max
>> >>>>>>>>> sphere
>> >>>>>>>>> radius!
>> >>>>>>>>> ------
>> >>>>>>>>>
>> >>>>>>>>> was substituted with err/warning ?
>> >>>>>>>>>
>> >>>>>>>>> #0 no ERR writtent in mdout, ERR written in standard output
>> >>>>>>>>> (nohup.out)
>> >>>>>>>>> -----
>> >>>>>>>>> Nonbond cells need to be recalculated, restart simulation from
>> >>>>>>>>> previous
>> >>>>>>>>> checkpoint
>> >>>>>>>>> with a higher value for skinnb.
>> >>>>>>>>>
>> >>>>>>>>> -----
>> >>>>>>>>>
>> >>>>>>>>> Another thing,
>> >>>>>>>>>
>> >>>>>>>>> recently I started on another machine and GTX 580 GPU
>> simulation
>> >>>>>>>>> of
>> >>>>>>>>> relatively
>> >>>>>>>>> big system ( 364275 atoms/PME ). The system is composed also
>> from
>> >>>>>>>>> the
>> >>>>>>>>> "exotic" molecules like polymers. ff12SB, gaff, GLYCAM
>> >>>>>>>>> forcefields
>> >>>>>>>>> used
>> >>>>>>>>> here. I had problem even with minimization part here, having
>> big
>> >>>>>>>>> energy
>> >>>>>>>>> on the start:
>> >>>>>>>>>
>> >>>>>>>>> -----
>> >>>>>>>>> NSTEP ENERGY RMS GMAX
>> NAME
>> >>>>>>>>> NUMBER
>> >>>>>>>>> 1 2.8442E+09 2.1339E+02 1.7311E+04 O
>> >>>>>>>>> 32998
>> >>>>>>>>>
>> >>>>>>>>> BOND = 11051.7467 ANGLE = 17720.4706 DIHED
>> =
>> >>>>>>>>> 18977.7584
>> >>>>>>>>> VDWAALS = ************* EEL = -1257709.6203 HBOND
>> =
>> >>>>>>>>> 0.0000
>> >>>>>>>>> 1-4 VDW = 7253.7412 1-4 EEL = 149867.0207 RESTRAINT
>> =
>> >>>>>>>>> 0.0000
>> >>>>>>>>>
>> >>>>>>>>> ----
>> >>>>>>>>>
>> >>>>>>>>> with no chance to minimize the system even with 50 000 steps
>> in
>> >>>>>>>>> both
>> >>>>>>>>> min cycles (with constrained and unconstrained solute) and
>> hence
>> >>>>>>>>> heating
>> >>>>>>>>> NVT
>> >>>>>>>>> crashed immediately even with very small dt. I patched Amber12
>> >>>>>>>>> here
>> >>>>>>>>> with
>> >>>>>>>>> the
>> >>>>>>>>> bugfix 18 and the minimization was done without any problem
>> with
>> >>>>>>>>> common
>> >>>>>>>>> 5000 steps
>> >>>>>>>>> (obtaining target Energy -1.4505E+06 while that initial was
>> that
>> >>>>>>>>> written
>> >>>>>>>>> above).
>> >>>>>>>>>
>> >>>>>>>>> So indeed bugfix 18 solved some issues, but unfortunately not
>> >>>>>>>>> those
>> >>>>>>>>> related to
>> >>>>>>>>> Titans.
>> >>>>>>>>>
>> >>>>>>>>> Here I will try to install cuda 5.5, recompile GPU Amber part
>> >>>>>>>>> with
>> >>>>>>>>> this
>> >>>>>>>>> new
>> >>>>>>>>> cuda version and repeat the 100K tests.
>> >>>>>>>>>
>> >>>>>>>>> Scott, let us know how finished your experiment with
>> >>>>>>>>> downclocking of
>> >>>>>>>>> Titan.
>> >>>>>>>>> Maybe the best choice would be here to flash Titan directly
>> with
>> >>>>>>>>> your
>> >>>>>>>>> K20c bios :))
>> >>>>>>>>>
>> >>>>>>>>> M.
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> Dne Sat, 01 Jun 2013 21:09:46 +0200 Marek Maly
>> >>>>>>>>> <marek.maly.ujep.cz>
>> >>>>>>>>> napsal/-a:
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> Hi,
>> >>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> first of all thanks for providing of your test results !
>> >>>>>>>>>>
>> >>>>>>>>>> It seems that your results are more or less similar to that
>> of
>> >>>>>>>>>> mine maybe with the exception of the results on FactorIX
>> tests
>> >>>>>>>>>> where I had perfect stability and 100% or close to 100%
>> >>>>>>>>>> reproducibility.
>> >>>>>>>>>>
>> >>>>>>>>>> Anyway the type of errs which you reported are the same
>> which I
>> >>>>>>>>>> obtained.
>> >>>>>>>>>>
>> >>>>>>>>>> So let's see if the bugfix 18 will help here (or at least on
>> NPT
>> >>>>>>>>>> tests)
>> >>>>>>>>>> or not. As I wrote just before few minutes, it seems that it
>> was
>> >>>>>>>>>> not
>> >>>>>>>>>> still
>> >>>>>>>>>> loaded
>> >>>>>>>>>> to the given server, although it's description is already
>> >>>>>>>>>> present
>> >>>>>>>>>> on
>> >>>>>>>>>> the
>> >>>>>>>>>> given
>> >>>>>>>>>> web page ( see
>> >>>>>>>>>> http://ambermd.org/bugfixes12.****html<
>> http://ambermd.org/bugfixes12.**html>
>> >>>>>>>>>> <http://ambermd.org/**bugfixes12.html<
>> http://ambermd.org/bugfixes12.html>
>> >>>>>>>>>> >).
>> >>>>>>>>>>
>> >>>>>>>>>> As you can see, this bugfix contains also changes in CPU code
>> >>>>>>>>>> although
>> >>>>>>>>>> the majority is devoted to GPU code, so perhaps the best will
>> >>>>>>>>>> be to
>> >>>>>>>>>> recompile
>> >>>>>>>>>> whole amber with this patch although this patch would be
>> perhaps
>> >>>>>>>>>> applied
>> >>>>>>>>>> even after just
>> >>>>>>>>>> GPU configure command ( i.e. ./configure -cuda -noX11 gnu )
>> but
>> >>>>>>>>>> after
>> >>>>>>>>>> consequent
>> >>>>>>>>>> building, just the GPU binaries will be updated. Anyway I
>> would
>> >>>>>>>>>> rather
>> >>>>>>>>>> recompile
>> >>>>>>>>>> whole Amber after this patch.
>> >>>>>>>>>>
>> >>>>>>>>>> Regarding to GPU test under linux you may try memtestG80
>> >>>>>>>>>> (please use the updated/patched version from here
>> >>>>>>>>>> https://github.com/ihaque/****memtestG80<
>> https://github.com/ihaque/**memtestG80>
>> >>>>>>>>>> <https://github.com/**ihaque/memtestG80<
>> https://github.com/ihaque/memtestG80>
>> >>>>>>>>>> >
>> >>>>>>>>>> )
>> >>>>>>>>>>
>> >>>>>>>>>> just use git command like:
>> >>>>>>>>>>
>> >>>>>>>>>> git clone
>> >>>>>>>>>> https://github.com/ihaque/****memtestG80.git<
>> https://github.com/ihaque/**memtestG80.git>
>> >>>>>>>>>> <https://github.**com/ihaque/memtestG80.git<
>> https://github.com/ihaque/memtestG80.git>
>> >>>>>>>>>> >**PATCHED_MEMTEST-G80
>> >>>>>>>>>>
>> >>>>>>>>>> to download all the files and save them into directory named
>> >>>>>>>>>> PATCHED_MEMTEST-G80.
>> >>>>>>>>>>
>> >>>>>>>>>> another possibility is to try perhaps similar (but maybe more
>> >>>>>>>>>> up to
>> >>>>>>>>>> date)
>> >>>>>>>>>> test
>> >>>>>>>>>> cuda_memtest (
>> >>>>>>>>>> http://sourceforge.net/****projects/cudagpumemtest/<
>> http://sourceforge.net/**projects/cudagpumemtest/>
>> >>>>>>>>>> <http:**//sourceforge.net/projects/**cudagpumemtest/<
>> http://sourceforge.net/projects/cudagpumemtest/>
>> >>>>>>>>>> >).
>> >>>>>>>>>>
>> >>>>>>>>>> regarding ig value: If ig is not present in mdin, the default
>> >>>>>>>>>> value
>> >>>>>>>>>> is
>> >>>>>>>>>> used
>> >>>>>>>>>> (e.g. 71277) if ig=-1 the random seed will be based on the
>> >>>>>>>>>> current
>> >>>>>>>>>> date
>> >>>>>>>>>> and time, and hence will be different for every run (not a
>> good
>> >>>>>>>>>> variant
>> >>>>>>>>>> for our testts). I simply deleted eventual ig records from
>> all
>> >>>>>>>>>> mdins
>> >>>>>>>>>> so
>> >>>>>>>>>> I
>> >>>>>>>>>> assume that in each run the default seed 71277 was
>> automatically
>> >>>>>>>>>> used.
>> >>>>>>>>>>
>> >>>>>>>>>> M.
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Dne Sat, 01 Jun 2013 20:26:16 +0200 ET <sketchfoot.gmail.com>
>> >>>>>>>>>> napsal/-a:
>> >>>>>>>>>>
>> >>>>>>>>>> Hi,
>> >>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> I've put the graphics card into a machine with the working
>> GTX
>> >>>>>>>>>>> titan
>> >>>>>>>>>>> that I
>> >>>>>>>>>>> mentioned earlier.
>> >>>>>>>>>>>
>> >>>>>>>>>>> The Nvidia driver version is: 133.30
>> >>>>>>>>>>>
>> >>>>>>>>>>> Amber version is:
>> >>>>>>>>>>> AmberTools version 13.03
>> >>>>>>>>>>> Amber version 12.16
>> >>>>>>>>>>>
>> >>>>>>>>>>> I ran 50k steps with the amber benchmark using ig=43689 on
>> both
>> >>>>>>>>>>> cards.
>> >>>>>>>>>>> For
>> >>>>>>>>>>> the purpose of discriminating between them, the card I
>> believe
>> >>>>>>>>>>> (fingers
>> >>>>>>>>>>> crossed) is working is called GPU-00_TeaNCake, whilst the
>> other
>> >>>>>>>>>>> one
>> >>>>>>>>>>> is
>> >>>>>>>>>>> called GPU-01_008.
>> >>>>>>>>>>>
>> >>>>>>>>>>> *When I run the tests on GPU-01_008:*
>> >>>>>>>>>>>
>> >>>>>>>>>>> 1) All the tests (across 2x repeats) finish apart from the
>> >>>>>>>>>>> following
>> >>>>>>>>>>> which
>> >>>>>>>>>>> have the errors listed:
>> >>>>>>>>>>>
>> >>>>>>>>>>> ------------------------------****--------------
>> >>>>>>>>>>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> >>>>>>>>>>> Error: unspecified launch failure launching kernel
>> kNLSkinTest
>> >>>>>>>>>>> cudaFree GpuBuffer::Deallocate failed unspecified launch
>> >>>>>>>>>>> failure
>> >>>>>>>>>>>
>> >>>>>>>>>>> ------------------------------****--------------
>> >>>>>>>>>>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> >>>>>>>>>>> cudaMemcpy GpuBuffer::Download failed unspecified launch
>> >>>>>>>>>>> failure
>> >>>>>>>>>>>
>> >>>>>>>>>>> ------------------------------****--------------
>> >>>>>>>>>>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> >>>>>>>>>>> Error: unspecified launch failure launching kernel
>> kNLSkinTest
>> >>>>>>>>>>> cudaFree GpuBuffer::Deallocate failed unspecified launch
>> >>>>>>>>>>> failure
>> >>>>>>>>>>>
>> >>>>>>>>>>> ------------------------------****--------------
>> >>>>>>>>>>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> >>>>>>>>>>> cudaMemcpy GpuBuffer::Download failed unspecified launch
>> >>>>>>>>>>> failure
>> >>>>>>>>>>> grep: mdinfo.1GTX680: No such file or directory
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> 2) The sdiff logs indicate that reproducibility across the
>> two
>> >>>>>>>>>>> repeats
>> >>>>>>>>>>> is
>> >>>>>>>>>>> as follows:
>> >>>>>>>>>>>
>> >>>>>>>>>>> *GB_myoglobin: *Reproducible across 50k steps
>> >>>>>>>>>>> *GB_nucleosome:* Reproducible till step 7400
>> >>>>>>>>>>> *GB_TRPCage:* Reproducible across 50k steps
>> >>>>>>>>>>>
>> >>>>>>>>>>> *PME_JAC_production_NVE: *No reproducibility shown from step
>> >>>>>>>>>>> 1,000
>> >>>>>>>>>>> onwards
>> >>>>>>>>>>> *PME_JAC_production_NPT*: Reproducible till step 1,000.
>> Also
>> >>>>>>>>>>> outfile
>> >>>>>>>>>>> is
>> >>>>>>>>>>> not written properly - blank gaps appear where something
>> should
>> >>>>>>>>>>> have
>> >>>>>>>>>>> been
>> >>>>>>>>>>> written
>> >>>>>>>>>>>
>> >>>>>>>>>>> *PME_FactorIX_production_NVE:* Reproducible across 50k steps
>> >>>>>>>>>>> *PME_FactorIX_production_NPT:* Reproducible across 50k steps
>> >>>>>>>>>>>
>> >>>>>>>>>>> *PME_Cellulose_production_NVE:***** Failure means that both
>> >>>>>>>>>>> runs
>> >>>>>>>>>>> do
>> >>>>>>>>>>> not
>> >>>>>>>>>>> finish
>> >>>>>>>>>>> (see point1)
>> >>>>>>>>>>> *PME_Cellulose_production_NPT: *Failure means that both
>> runs do
>> >>>>>>>>>>> not
>> >>>>>>>>>>> finish
>> >>>>>>>>>>> (see point1)
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> ##############################****############################**
>> >>>>>>>>>>> ##**
>> >>>>>>>>>>> ###########################
>> >>>>>>>>>>>
>> >>>>>>>>>>> *When I run the tests on * *GPU-00_TeaNCake:*
>> >>>>>>>>>>> *
>> >>>>>>>>>>> *
>> >>>>>>>>>>> 1) All the tests (across 2x repeats) finish apart from the
>> >>>>>>>>>>> following
>> >>>>>>>>>>> which
>> >>>>>>>>>>> have the errors listed:
>> >>>>>>>>>>> ------------------------------****-------
>> >>>>>>>>>>> JAC_PRODUCTION_NPT - 23,558 atoms PME
>> >>>>>>>>>>> PMEMD Terminated Abnormally!
>> >>>>>>>>>>> ------------------------------****-------
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> 2) The sdiff logs indicate that reproducibility across the
>> two
>> >>>>>>>>>>> repeats
>> >>>>>>>>>>> is
>> >>>>>>>>>>> as follows:
>> >>>>>>>>>>>
>> >>>>>>>>>>> *GB_myoglobin:* Reproducible across 50k steps
>> >>>>>>>>>>> *GB_nucleosome:* Reproducible across 50k steps
>> >>>>>>>>>>> *GB_TRPCage:* Reproducible across 50k steps
>> >>>>>>>>>>>
>> >>>>>>>>>>> *PME_JAC_production_NVE:* No reproducibility shown from step
>> >>>>>>>>>>> 10,000
>> >>>>>>>>>>> onwards
>> >>>>>>>>>>> *PME_JAC_production_NPT: * No reproducibility shown from
>> step
>> >>>>>>>>>>> 10,000
>> >>>>>>>>>>> onwards. Also outfile is not written properly - blank gaps
>> >>>>>>>>>>> appear
>> >>>>>>>>>>> where
>> >>>>>>>>>>> something should have been written. Repeat 2 Crashes with
>> error
>> >>>>>>>>>>> noted
>> >>>>>>>>>>> in
>> >>>>>>>>>>> 1.
>> >>>>>>>>>>>
>> >>>>>>>>>>> *PME_FactorIX_production_NVE:* No reproducibility shown from
>> >>>>>>>>>>> step
>> >>>>>>>>>>> 9,000
>> >>>>>>>>>>> onwards
>> >>>>>>>>>>> *PME_FactorIX_production_NPT: *Reproducible across 50k steps
>> >>>>>>>>>>>
>> >>>>>>>>>>> *PME_Cellulose_production_NVE: *No reproducibility shown
>> from
>> >>>>>>>>>>> step
>> >>>>>>>>>>> 5,000
>> >>>>>>>>>>> onwards
>> >>>>>>>>>>> *PME_Cellulose_production_NPT: ** *No reproducibility shown
>> >>>>>>>>>>> from
>> >>>>>>>>>>> step
>> >>>>>>>>>>> 29,000 onwards. Also outfile is not written properly - blank
>> >>>>>>>>>>> gaps
>> >>>>>>>>>>> appear
>> >>>>>>>>>>> where something should have been written.
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> Out files and sdiff files are included as attatchments
>> >>>>>>>>>>>
>> >>>>>>>>>>> ##############################****###################
>> >>>>>>>>>>>
>> >>>>>>>>>>> So I'm going to update my nvidia driver to the latest
>> version
>> >>>>>>>>>>> and
>> >>>>>>>>>>> patch
>> >>>>>>>>>>> amber to the latest version and rerun the tests to see if
>> >>>>>>>>>>> there is
>> >>>>>>>>>>> any
>> >>>>>>>>>>> improvement. Could someone let me know if it is necessary to
>> >>>>>>>>>>> recompile
>> >>>>>>>>>>> any
>> >>>>>>>>>>> or all of AMBER after applying the bugfixes?
>> >>>>>>>>>>>
>> >>>>>>>>>>> Additionally, I'm going to run memory tests and heaven
>> >>>>>>>>>>> benchmarks
>> >>>>>>>>>>> on
>> >>>>>>>>>>> the
>> >>>>>>>>>>> cards to check whether they are faulty or not.
>> >>>>>>>>>>>
>> >>>>>>>>>>> I'm thinking that there is a mix of hardware
>> >>>>>>>>>>> error/configuration
>> >>>>>>>>>>> (esp
>> >>>>>>>>>>> in
>> >>>>>>>>>>> the case of GPU-01_008) and amber software error in this
>> >>>>>>>>>>> situation.
>> >>>>>>>>>>> What
>> >>>>>>>>>>> do
>> >>>>>>>>>>> you guys think?
>> >>>>>>>>>>>
>> >>>>>>>>>>> Also am I right in thinking (from what Scott was saying)
>> that
>> >>>>>>>>>>> all
>> >>>>>>>>>>> the
>> >>>>>>>>>>> benchmarks should be reproducible across 50k steps but
>> begin to
>> >>>>>>>>>>> diverge
>> >>>>>>>>>>> at
>> >>>>>>>>>>> around 100K steps? Is there any difference from in setting
>> *ig
>> >>>>>>>>>>> *to
>> >>>>>>>>>>> an
>> >>>>>>>>>>> explicit number to removing it from the mdin file?
>> >>>>>>>>>>>
>> >>>>>>>>>>> br,
>> >>>>>>>>>>> g
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> On 31 May 2013 23:45, ET <sketchfoot.gmail.com> wrote:
>> >>>>>>>>>>>
>> >>>>>>>>>>> I don't need sysadmins, but sysadmins need me as it gives
>> >>>>>>>>>>> purpose
>> >>>>>>>>>>> to
>> >>>>>>>>>>>
>> >>>>>>>>>>>> their
>> >>>>>>>>>>>> bureaucratic existence. A encountered evil if working in an
>> >>>>>>>>>>>> institution
>> >>>>>>>>>>>> or
>> >>>>>>>>>>>> comapny IMO. Good science and indiviguality being
>> sacrificed
>> >>>>>>>>>>>> for
>> >>>>>>>>>>>> standardisation and mediocrity in the intrerests of
>> maintaing
>> >>>>>>>>>>>> a
>> >>>>>>>>>>>> system
>> >>>>>>>>>>>> that
>> >>>>>>>>>>>> focusses on maintaining the system and not the objective.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> You need root to move fwd on these things, unfortunately.
>> and
>> >>>>>>>>>>>> ppl
>> >>>>>>>>>>>> with
>> >>>>>>>>>>>> root are kinda like your parents when you try to borrow
>> money
>> >>>>>>>>>>>> from
>> >>>>>>>>>>>> them
>> >>>>>>>>>>>> .
>> >>>>>>>>>>>> age 12 :D
>> >>>>>>>>>>>> On May 31, 2013 9:34 PM, "Marek Maly" <marek.maly.ujep.cz>
>> >>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Sorry why do you need sysadmins :)) ?
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> BTW here is the most recent driver:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> http://www.nvidia.com/object/****linux-display-amd64-319.23-**<
>> http://www.nvidia.com/object/**linux-display-amd64-319.23-**>
>> >>>>>>>>>>>>>
>> driver.html<http://www.nvidia.**com/object/linux-display-**
>> >>>>>>>>>>>>> amd64-319.23-driver.html<
>> http://www.nvidia.com/object/linux-display-amd64-319.23-driver.html>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I do not remember anything easier than is to install
>> driver
>> >>>>>>>>>>>>> (especially
>> >>>>>>>>>>>>> in case of binary (*.run) installer) :))
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> M.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Dne Fri, 31 May 2013 22:02:34 +0200 ET
>> <sketchfoot.gmail.com
>> >
>> >>>>>>>>>>>>> napsal/-a:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> > Yup. I know. I replaced a 680 and the everknowing
>> sysadmins
>> >>>>>>>>>>>>> are
>> >>>>>>>>>>>>> reluctant
>> >>>>>>>>>>>>> > to install drivers not in the repositoery as they are
>> >>>>>>>>>>>>> lame. :(
>> >>>>>>>>>>>>> > On May 31, 2013 7:14 PM, "Marek Maly"
>> <marek.maly.ujep.cz>
>> >>>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> As I already wrote you,
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> the first driver which properly/officially supports
>> >>>>>>>>>>>>> Titans,
>> >>>>>>>>>>>>> should
>> >>>>>>>>>>>>> be
>> >>>>>>>>>>>>> >> 313.26 .
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> Anyway I am curious mainly about your 100K repetitive
>> >>>>>>>>>>>>> tests
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> >> your Titan SC card. Especially in case of these tests (
>> >>>>>>>>>>>>> JAC_NVE,
>> >>>>>>>>>>>>> JAC_NPT
>> >>>>>>>>>>>>> >> and CELLULOSE_NVE ) where
>> >>>>>>>>>>>>> >> my Titans SC randomly failed or succeeded. In
>> >>>>>>>>>>>>> FACTOR_IX_NVE,
>> >>>>>>>>>>>>> >> FACTOR_IX_NPT
>> >>>>>>>>>>>>> >> tests both
>> >>>>>>>>>>>>> >> my cards are perfectly stable (independently from drv.
>> >>>>>>>>>>>>> version)
>> >>>>>>>>>>>>> and
>> >>>>>>>>>>>>> also
>> >>>>>>>>>>>>> >> the runs
>> >>>>>>>>>>>>> >> are perfectly or almost perfectly reproducible.
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> Also if your test will crash please report the eventual
>> >>>>>>>>>>>>> errs.
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> To this moment I have this actual library of errs on my
>> >>>>>>>>>>>>> Titans
>> >>>>>>>>>>>>> SC
>> >>>>>>>>>>>>> GPUs.
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> #1 ERR writtent in mdout:
>> >>>>>>>>>>>>> >> ------
>> >>>>>>>>>>>>> >> | ERROR: max pairlist cutoff must be less than unit
>> cell
>> >>>>>>>>>>>>> max
>> >>>>>>>>>>>>> sphere
>> >>>>>>>>>>>>> >> radius!
>> >>>>>>>>>>>>> >> ------
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> #2 no ERR writtent in mdout, ERR written in standard
>> >>>>>>>>>>>>> output
>> >>>>>>>>>>>>> (nohup.out)
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> ----
>> >>>>>>>>>>>>> >> Error: unspecified launch failure launching kernel
>> >>>>>>>>>>>>> kNLSkinTest
>> >>>>>>>>>>>>> >> cudaFree GpuBuffer::Deallocate failed unspecified
>> launch
>> >>>>>>>>>>>>> failure
>> >>>>>>>>>>>>> >> ----
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> #3 no ERR writtent in mdout, ERR written in standard
>> >>>>>>>>>>>>> output
>> >>>>>>>>>>>>> (nohup.out)
>> >>>>>>>>>>>>> >> ----
>> >>>>>>>>>>>>> >> cudaMemcpy GpuBuffer::Download failed unspecified
>> launch
>> >>>>>>>>>>>>> failure
>> >>>>>>>>>>>>> >> ----
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> Another question, regarding your Titan SC, it is also
>> >>>>>>>>>>>>> EVGA as
>> >>>>>>>>>>>>> in
>> >>>>>>>>>>>>> my
>> >>>>>>>>>>>>> case
>> >>>>>>>>>>>>> >> or it is another producer ?
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> Thanks,
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> M.
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> Dne Fri, 31 May 2013 19:17:03 +0200 ET
>> >>>>>>>>>>>>> <sketchfoot.gmail.com
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> napsal/-a:
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> > Well, this is interesting...
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > I ran 50k steps on the Titan on the other machine
>> with
>> >>>>>>>>>>>>> driver
>> >>>>>>>>>>>>> 310.44
>> >>>>>>>>>>>>> >> and
>> >>>>>>>>>>>>> >> > it
>> >>>>>>>>>>>>> >> > passed all the GB steps. i.e totally identical
>> results
>> >>>>>>>>>>>>> over
>> >>>>>>>>>>>>> two
>> >>>>>>>>>>>>> >> repeats.
>> >>>>>>>>>>>>> >> > However, it failed all the PME tests after step 1000.
>> >>>>>>>>>>>>> I'm
>> >>>>>>>>>>>>> going
>> >>>>>>>>>>>>> to
>> >>>>>>>>>>>>> > update
>> >>>>>>>>>>>>> >> > the driver and test it again.
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > Files included as attachments.
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > br,
>> >>>>>>>>>>>>> >> > g
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > On 31 May 2013 16:40, Marek Maly <marek.maly.ujep.cz>
>> >>>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> >> One more thing,
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> can you please check under which frequency is
>> running
>> >>>>>>>>>>>>> that
>> >>>>>>>>>>>>> your
>> >>>>>>>>>>>>> >> titan ?
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> As the base frequency of normal Titans is 837MHz and
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> Boost
>> >>>>>>>>>>>>> one
>> >>>>>>>>>>>>> is
>> >>>>>>>>>>>>> >> >> 876MHz I
>> >>>>>>>>>>>>> >> >> assume that yor GPU is running automatically also
>> under
>> >>>>>>>>>>>>> it's
>> >>>>>>>>>>>>> boot
>> >>>>>>>>>>>>> >> >> frequency (876MHz).
>> >>>>>>>>>>>>> >> >> You can find this information e.g. in Amber mdout
>> file.
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> You also mentioned some crashes in your previous
>> email.
>> >>>>>>>>>>>>> Your
>> >>>>>>>>>>>>> ERRs
>> >>>>>>>>>>>>> >> were
>> >>>>>>>>>>>>> >> >> something like those here:
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> #1 ERR writtent in mdout:
>> >>>>>>>>>>>>> >> >> ------
>> >>>>>>>>>>>>> >> >> | ERROR: max pairlist cutoff must be less than
>> unit
>> >>>>>>>>>>>>> cell
>> >>>>>>>>>>>>> max
>> >>>>>>>>>>>>> sphere
>> >>>>>>>>>>>>> >> >> radius!
>> >>>>>>>>>>>>> >> >> ------
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> #2 no ERR writtent in mdout, ERR written in standard
>> >>>>>>>>>>>>> output
>> >>>>>>>>>>>>> >> (nohup.out)
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> ----
>> >>>>>>>>>>>>> >> >> Error: unspecified launch failure launching kernel
>> >>>>>>>>>>>>> kNLSkinTest
>> >>>>>>>>>>>>> >> >> cudaFree GpuBuffer::Deallocate failed unspecified
>> >>>>>>>>>>>>> launch
>> >>>>>>>>>>>>> failure
>> >>>>>>>>>>>>> >> >> ----
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> #3 no ERR writtent in mdout, ERR written in standard
>> >>>>>>>>>>>>> output
>> >>>>>>>>>>>>> >> (nohup.out)
>> >>>>>>>>>>>>> >> >> ----
>> >>>>>>>>>>>>> >> >> cudaMemcpy GpuBuffer::Download failed unspecified
>> >>>>>>>>>>>>> launch
>> >>>>>>>>>>>>> failure
>> >>>>>>>>>>>>> >> >> ----
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> or you obtained some new/additional errs ?
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> M.
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> Dne Fri, 31 May 2013 17:30:57 +0200 filip fratev
>> >>>>>>>>>>>>> >> <filipfratev.yahoo.com
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> >> napsal/-a:
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> > Hi,
>> >>>>>>>>>>>>> >> >> > This is what I obtained for 50K tests and "normal"
>> >>>>>>>>>>>>> GTXTitan:
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > run1:
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------*
>> >>>>>>>>>>>>> *--**
>> >>>>>>>>>>>>> ------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > A V E R A G E S O V E R 50 S T E P S
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>>>>>>>>>>>> 299.87
>> >>>>>>>>>>>>> >> PRESS
>> >>>>>>>>>>>>> >> >> > = 0.0
>> >>>>>>>>>>>>> >> >> > Etot = -443237.1079 EKtot = 257679.9750
>> >>>>>>>>>>>>> EPtot
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > -700917.0829
>> >>>>>>>>>>>>> >> >> > BOND = 20193.1856 ANGLE = 53517.5432
>> >>>>>>>>>>>>> DIHED
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 23575.4648
>> >>>>>>>>>>>>> >> >> > 1-4 NB = 21759.5524 1-4 EEL = 742552.5939
>> >>>>>>>>>>>>> VDWAALS
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 96286.7714
>> >>>>>>>>>>>>> >> >> > EELEC = -1658802.1941 EHBOND = 0.0000
>> >>>>>>>>>>>>> RESTRAINT
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 0.0000
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------
>> >>>>>>>>>>>>> **--**
>> >>>>>>>>>>>>> ------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > R M S F L U C T U A T I O N S
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>>>>>>>>>>>> 0.33
>> >>>>>>>>>>>>> >> PRESS
>> >>>>>>>>>>>>> >> >> > = 0.0
>> >>>>>>>>>>>>> >> >> > Etot = 11.2784 EKtot = 284.8999
>> >>>>>>>>>>>>> EPtot
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 289.0773
>> >>>>>>>>>>>>> >> >> > BOND = 136.3417 ANGLE = 214.0054
>> >>>>>>>>>>>>> DIHED
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 59.4893
>> >>>>>>>>>>>>> >> >> > 1-4 NB = 58.5891 1-4 EEL = 330.5400
>> >>>>>>>>>>>>> VDWAALS
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 559.2079
>> >>>>>>>>>>>>> >> >> > EELEC = 743.8771 EHBOND = 0.0000
>> >>>>>>>>>>>>> RESTRAINT
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 0.0000
>> >>>>>>>>>>>>> >> >> > |E(PBS) = 21.8119
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------
>> >>>>>>>>>>>>> **--**
>> >>>>>>>>>>>>> ------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > run2:
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------*
>> >>>>>>>>>>>>> *--**
>> >>>>>>>>>>>>> ------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > A V E R A G E S O V E R 50 S T E P S
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>>>>>>>>>>>> 299.89
>> >>>>>>>>>>>>> >> PRESS
>> >>>>>>>>>>>>> >> >> > = 0.0
>> >>>>>>>>>>>>> >> >> > Etot = -443240.0999 EKtot = 257700.0950
>> >>>>>>>>>>>>> EPtot
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > -700940.1949
>> >>>>>>>>>>>>> >> >> > BOND = 20241.9174 ANGLE = 53644.6694
>> >>>>>>>>>>>>> DIHED
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 23541.3737
>> >>>>>>>>>>>>> >> >> > 1-4 NB = 21803.1898 1-4 EEL = 742754.2254
>> >>>>>>>>>>>>> VDWAALS
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 96298.8308
>> >>>>>>>>>>>>> >> >> > EELEC = -1659224.4013 EHBOND = 0.0000
>> >>>>>>>>>>>>> RESTRAINT
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 0.0000
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------
>> >>>>>>>>>>>>> **--**
>> >>>>>>>>>>>>> ------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > R M S F L U C T U A T I O N S
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>>>>>>>>>>>> 0.41
>> >>>>>>>>>>>>> >> PRESS
>> >>>>>>>>>>>>> >> >> > = 0.0
>> >>>>>>>>>>>>> >> >> > Etot = 10.7633 EKtot = 348.2819
>> >>>>>>>>>>>>> EPtot
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 353.9918
>> >>>>>>>>>>>>> >> >> > BOND = 106.5314 ANGLE = 196.7052
>> >>>>>>>>>>>>> DIHED
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 69.7476
>> >>>>>>>>>>>>> >> >> > 1-4 NB = 60.3435 1-4 EEL = 400.7466
>> >>>>>>>>>>>>> VDWAALS
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 462.7763
>> >>>>>>>>>>>>> >> >> > EELEC = 651.9857 EHBOND = 0.0000
>> >>>>>>>>>>>>> RESTRAINT
>> >>>>>>>>>>>>> =
>> >>>>>>>>>>>>> >> >> > 0.0000
>> >>>>>>>>>>>>> >> >> > |E(PBS) = 17.0642
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------
>> >>>>>>>>>>>>> **--**
>> >>>>>>>>>>>>> ------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> ------------------------------****----------------------------*
>> >>>>>>>>>>>>> *--**
>> >>>>>>>>>>>>> --------------------
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > ______________________________****__
>> >>>>>>>>>>>>> >> >> > From: Marek Maly <marek.maly.ujep.cz>
>> >>>>>>>>>>>>> >> >> > To: AMBER Mailing List <amber.ambermd.org>
>> >>>>>>>>>>>>> >> >> > Sent: Friday, May 31, 2013 3:34 PM
>> >>>>>>>>>>>>> >> >> > Subject: Re: [AMBER] experiences with EVGA GTX
>> TITAN
>> >>>>>>>>>>>>> Superclocked
>> >>>>>>>>>>>>> -
>> >>>>>>>>>>>>> >> >> > memtestG80 - UNDERclocking in Linux ?
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > Hi here are my 100K results for driver 313.30 (and
>> >>>>>>>>>>>>> still
>> >>>>>>>>>>>>> Cuda
>> >>>>>>>>>>>>> 5.0).
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > The results are rather similar to those obtained
>> >>>>>>>>>>>>> >> >> > under my original driver 319.17 (see the first
>> table
>> >>>>>>>>>>>>> >> >> > which I sent in this thread).
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > M.
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> > Dne Fri, 31 May 2013 12:29:59 +0200 Marek Maly <
>> >>>>>>>>>>>>> marek.maly.ujep.cz>
>> >>>>>>>>>>>>> >> >> > napsal/-a:
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >> Hi,
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> please try to run at lest 100K tests twice to
>> verify
>> >>>>>>>>>>>>> exact
>> >>>>>>>>>>>>> >> >> >> reproducibility
>> >>>>>>>>>>>>> >> >> >> of the results on the given card. If you find in
>> any
>> >>>>>>>>>>>>> mdin
>> >>>>>>>>>>>>> file
>> >>>>>>>>>>>>> >> ig=-1
>> >>>>>>>>>>>>> >> >> >> just
>> >>>>>>>>>>>>> >> >> >> delete it to ensure that you are using the
>> identical
>> >>>>>>>>>>>>> random
>> >>>>>>>>>>>>> seed
>> >>>>>>>>>>>>> >> for
>> >>>>>>>>>>>>> >> >> >> both
>> >>>>>>>>>>>>> >> >> >> runs. You can eventually omit NUCLEOSOME test
>> >>>>>>>>>>>>> >> >> >> as it is too much time consuming.
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> Driver 310.44 ?????
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> As far as I know the proper support for titans is
>> >>>>>>>>>>>>> from
>> >>>>>>>>>>>>> version
>> >>>>>>>>>>>>> > 313.26
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> see e.g. here :
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> http://www.geeks3d.com/****20130306/nvidia-releases-r313-****<
>> http://www.geeks3d.com/**20130306/nvidia-releases-r313-**>
>> >>>>>>>>>>>>>
>> 26-for-linux-with-gtx-titan-****support/<http://www.geeks3d.
>> **
>> >>>>>>>>>>>>>
>> com/20130306/nvidia-releases-**r313-26-for-linux-with-gtx-**
>> >>>>>>>>>>>>> titan-support/<
>> http://www.geeks3d.com/20130306/nvidia-releases-r313-26-for-linux-with-gtx-titan-support/
>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> BTW: On my site downgrade to drv. 313.30 did not
>> >>>>>>>>>>>>> solved
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> situation, I
>> >>>>>>>>>>>>> >> >> >> will post
>> >>>>>>>>>>>>> >> >> >> my results soon here.
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> M.
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >> Dne Fri, 31 May 2013 12:21:21 +0200 ET <
>> >>>>>>>>>>>>> sketchfoot.gmail.com>
>> >>>>>>>>>>>>> >> >> napsal/-a:
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>> ps. I have another install of amber on another
>> >>>>>>>>>>>>> computer
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> a
>> >>>>>>>>>>>>> >> >> >>> different
>> >>>>>>>>>>>>> >> >> >>> Titan and different Driver Version: 310.44.
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>> In the interests of thrashing the proverbial
>> horse,
>> >>>>>>>>>>>>> I'll
>> >>>>>>>>>>>>> run
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> >>> benchmark
>> >>>>>>>>>>>>> >> >> >>> for 50k steps. :P
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>> br,
>> >>>>>>>>>>>>> >> >> >>> g
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>> On 31 May 2013 11:17, ET <sketchfoot.gmail.com>
>> >>>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>>> Hi, I just ran the Amber benchmark for the
>> default
>> >>>>>>>>>>>>> (10000
>> >>>>>>>>>>>>> steps)
>> >>>>>>>>>>>>> >> >> on my
>> >>>>>>>>>>>>> >> >> >>>> Titan.
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>> Using sdiff -sB showed that the two runs were
>> >>>>>>>>>>>>> completely
>> >>>>>>>>>>>>> > identical.
>> >>>>>>>>>>>>> >> >> >>>> I've
>> >>>>>>>>>>>>> >> >> >>>> attached compressed files of the mdout & diff
>> >>>>>>>>>>>>> files.
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>> br,
>> >>>>>>>>>>>>> >> >> >>>> g
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>> On 30 May 2013 23:41, Marek Maly
>> >>>>>>>>>>>>> <marek.maly.ujep.cz
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>>> OK, let's see. The eventual downclocking I
>> see as
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> very
>> >>>>>>>>>>>>> last
>> >>>>>>>>>>>>> >> >> >>>>> possibility
>> >>>>>>>>>>>>> >> >> >>>>> (if I don't decide for RMAing). But now still
>> >>>>>>>>>>>>> some
>> >>>>>>>>>>>>> other
>> >>>>>>>>>>>>> >> >> experiments
>> >>>>>>>>>>>>> >> >> >>>>> are
>> >>>>>>>>>>>>> >> >> >>>>> available :))
>> >>>>>>>>>>>>> >> >> >>>>> I just started 100K tests under 313.30 driver.
>> >>>>>>>>>>>>> For
>> >>>>>>>>>>>>> today
>> >>>>>>>>>>>>> good
>> >>>>>>>>>>>>> >> >> night
>> >>>>>>>>>>>>> >> >> >>>>> ...
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> M.
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> Dne Fri, 31 May 2013 00:45:49 +0200 Scott Le
>> >>>>>>>>>>>>> Grand
>> >>>>>>>>>>>>> >> >> >>>>> <varelse2005.gmail.com
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> napsal/-a:
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> > It will be very interesting if this behavior
>> >>>>>>>>>>>>> persists
>> >>>>>>>>>>>>> after
>> >>>>>>>>>>>>> >> >> >>>>> downclocking.
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> > But right now, Titan 0 *looks* hosed and
>> Titan
>> >>>>>>>>>>>>> 1
>> >>>>>>>>>>>>> *looks*
>> >>>>>>>>>>>>> like
>> >>>>>>>>>>>>> > it
>> >>>>>>>>>>>>> >> >> >>>>> needs
>> >>>>>>>>>>>>> >> >> >>>>> > downclocking...
>> >>>>>>>>>>>>> >> >> >>>>> > On May 30, 2013 3:20 PM, "Marek Maly"
>> >>>>>>>>>>>>> <marek.maly.ujep.cz>
>> >>>>>>>>>>>>> >> >> wrote:
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >> Hi all,
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> here are my results from the 500K steps 2 x
>> >>>>>>>>>>>>> repeated
>> >>>>>>>>>>>>> > benchmarks
>> >>>>>>>>>>>>> >> >> >>>>> >> under 319.23 driver and still Cuda 5.0 (see
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> attached
>> >>>>>>>>>>>>> >> table
>> >>>>>>>>>>>>> >> >> ).
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> It is hard to say if the results are
>> better or
>> >>>>>>>>>>>>> worse
>> >>>>>>>>>>>>> than
>> >>>>>>>>>>>>> in
>> >>>>>>>>>>>>> > my
>> >>>>>>>>>>>>> >> >> >>>>> >> previous 100K test under driver 319.17.
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> While results from Cellulose test were
>> >>>>>>>>>>>>> improved
>> >>>>>>>>>>>>> and
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> > TITAN_1
>> >>>>>>>>>>>>> >> >> >>>>> card
>> >>>>>>>>>>>>> >> >> >>>>> >> even
>> >>>>>>>>>>>>> >> >> >>>>> >> successfully finished all 500K steps
>> moreover
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> exactly
>> >>>>>>>>>>>>> >> the
>> >>>>>>>>>>>>> >> >> >>>>> same
>> >>>>>>>>>>>>> >> >> >>>>> >> final
>> >>>>>>>>>>>>> >> >> >>>>> >> energy !
>> >>>>>>>>>>>>> >> >> >>>>> >> (TITAN_0 at least finished more than 100K
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> and in
>> >>>>>>>>>>>>> >> RUN_01
>> >>>>>>>>>>>>> >> >> even
>> >>>>>>>>>>>>> >> >> >>>>> more
>> >>>>>>>>>>>>> >> >> >>>>> >> than 400K steps)
>> >>>>>>>>>>>>> >> >> >>>>> >> In JAC_NPT test no GPU was able to finish
>> at
>> >>>>>>>>>>>>> least
>> >>>>>>>>>>>>> 100K
>> >>>>>>>>>>>>> >> steps
>> >>>>>>>>>>>>> >> >> and
>> >>>>>>>>>>>>> >> >> >>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> >> results from JAC_NVE
>> >>>>>>>>>>>>> >> >> >>>>> >> test are also not too much convincing.
>> >>>>>>>>>>>>> FACTOR_IX_NVE
>> >>>>>>>>>>>>> and
>> >>>>>>>>>>>>> >> >> >>>>> FACTOR_IX_NPT
>> >>>>>>>>>>>>> >> >> >>>>> >> were successfully
>> >>>>>>>>>>>>> >> >> >>>>> >> finished with 100% reproducibility in
>> >>>>>>>>>>>>> FACTOR_IX_NPT
>> >>>>>>>>>>>>> case
>> >>>>>>>>>>>>> >> (on
>> >>>>>>>>>>>>> >> >> both
>> >>>>>>>>>>>>> >> >> >>>>> >> cards)
>> >>>>>>>>>>>>> >> >> >>>>> >> and almost
>> >>>>>>>>>>>>> >> >> >>>>> >> 100% reproducibility in case of
>> FACTOR_IX_NVE
>> >>>>>>>>>>>>> (again
>> >>>>>>>>>>>>> 100%
>> >>>>>>>>>>>>> in
>> >>>>>>>>>>>>> >> >> case
>> >>>>>>>>>>>>> >> >> >>>>> of
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_1). TRPCAGE, MYOGLOBIN
>> >>>>>>>>>>>>> >> >> >>>>> >> again finished without any problem with
>> 100%
>> >>>>>>>>>>>>> >> reproducibility.
>> >>>>>>>>>>>>> >> >> >>>>> NUCLEOSOME
>> >>>>>>>>>>>>> >> >> >>>>> >> test was not done
>> >>>>>>>>>>>>> >> >> >>>>> >> this time due to high time requirements. If
>> >>>>>>>>>>>>> you
>> >>>>>>>>>>>>> find
>> >>>>>>>>>>>>> in
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> table
>> >>>>>>>>>>>>> >> >> >>>>> >> positive
>> >>>>>>>>>>>>> >> >> >>>>> >> number finishing with
>> >>>>>>>>>>>>> >> >> >>>>> >> K (which means "thousands") it means the
>> last
>> >>>>>>>>>>>>> number
>> >>>>>>>>>>>>> of
>> >>>>>>>>>>>>> step
>> >>>>>>>>>>>>> >> >> >>>>> written in
>> >>>>>>>>>>>>> >> >> >>>>> >> mdout before crash.
>> >>>>>>>>>>>>> >> >> >>>>> >> Below are all the 3 types of detected errs
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> relevant
>> >>>>>>>>>>>>> >> >> >>>>> systems/rounds
>> >>>>>>>>>>>>> >> >> >>>>> >> where the given err
>> >>>>>>>>>>>>> >> >> >>>>> >> appeared.
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> Now I will try just 100K tests under ETs
>> >>>>>>>>>>>>> favourite
>> >>>>>>>>>>>>> driver
>> >>>>>>>>>>>>> >> >> version
>> >>>>>>>>>>>>> >> >> >>>>> 313.30
>> >>>>>>>>>>>>> >> >> >>>>> >> :)) and then
>> >>>>>>>>>>>>> >> >> >>>>> >> I will eventually try to experiment with
>> cuda
>> >>>>>>>>>>>>> 5.5
>> >>>>>>>>>>>>> which
>> >>>>>>>>>>>>> I
>> >>>>>>>>>>>>> >> >> already
>> >>>>>>>>>>>>> >> >> >>>>> >> downloaded from the
>> >>>>>>>>>>>>> >> >> >>>>> >> cuda zone ( I had to become cuda developer
>> for
>> >>>>>>>>>>>>> this
>> >>>>>>>>>>>>> :))
>> >>>>>>>>>>>>> )
>> >>>>>>>>>>>>> >> BTW
>> >>>>>>>>>>>>> >> >> ET
>> >>>>>>>>>>>>> >> >> >>>>> thanks
>> >>>>>>>>>>>>> >> >> >>>>> >> for the frequency info !
>> >>>>>>>>>>>>> >> >> >>>>> >> and I am still ( perhaps not alone :)) )
>> very
>> >>>>>>>>>>>>> curious
>> >>>>>>>>>>>>> about
>> >>>>>>>>>>>>> >> >> your 2
>> >>>>>>>>>>>>> >> >> >>>>> x
>> >>>>>>>>>>>>> >> >> >>>>> >> repeated Amber benchmark tests with
>> >>>>>>>>>>>>> superclocked
>> >>>>>>>>>>>>> Titan.
>> >>>>>>>>>>>>> >> Indeed
>> >>>>>>>>>>>>> >> >> >>>>> that
>> >>>>>>>>>>>>> >> >> >>>>> I
>> >>>>>>>>>>>>> >> >> >>>>> am
>> >>>>>>>>>>>>> >> >> >>>>> >> very curious also about that Ross "hot"
>> patch.
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> M.
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> ERRORS DETECTED DURING THE 500K steps tests
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> driver
>> >>>>>>>>>>>>> >> 319.23
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> #1 ERR writtent in mdout:
>> >>>>>>>>>>>>> >> >> >>>>> >> ------
>> >>>>>>>>>>>>> >> >> >>>>> >> | ERROR: max pairlist cutoff must be less
>> >>>>>>>>>>>>> than
>> >>>>>>>>>>>>> unit
>> >>>>>>>>>>>>> cell
>> >>>>>>>>>>>>> >> max
>> >>>>>>>>>>>>> >> >> >>>>> sphere
>> >>>>>>>>>>>>> >> >> >>>>> >> radius!
>> >>>>>>>>>>>>> >> >> >>>>> >> ------
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_1 JAC_NPT (at least 5000
>> steps
>> >>>>>>>>>>>>> successfully
>> >>>>>>>>>>>>> > done
>> >>>>>>>>>>>>> >> >> >>>>> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NPT (at least 8000
>> steps
>> >>>>>>>>>>>>> successfully
>> >>>>>>>>>>>>> > done
>> >>>>>>>>>>>>> >> >> >>>>> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> #2 no ERR writtent in mdout, ERR written in
>> >>>>>>>>>>>>> standard
>> >>>>>>>>>>>>> output
>> >>>>>>>>>>>>> >> >> >>>>> (nohup.out)
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> ----
>> >>>>>>>>>>>>> >> >> >>>>> >> Error: unspecified launch failure launching
>> >>>>>>>>>>>>> kernel
>> >>>>>>>>>>>>> >> kNLSkinTest
>> >>>>>>>>>>>>> >> >> >>>>> >> cudaFree GpuBuffer::Deallocate failed
>> >>>>>>>>>>>>> unspecified
>> >>>>>>>>>>>>> launch
>> >>>>>>>>>>>>> >> >> failure
>> >>>>>>>>>>>>> >> >> >>>>> >> ----
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_1 CELLULOSE_NVE (at least 437
>> >>>>>>>>>>>>> 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> >> >> successfully
>> >>>>>>>>>>>>> >> >> >>>>> done
>> >>>>>>>>>>>>> >> >> >>>>> >> before crash)
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NVE (at least 162 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> >> successfully
>> >>>>>>>>>>>>> >> >> done
>> >>>>>>>>>>>>> >> >> >>>>> >> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 CELLULOSE_NVE (at least 117
>> >>>>>>>>>>>>> 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> >> >> successfully
>> >>>>>>>>>>>>> >> >> >>>>> done
>> >>>>>>>>>>>>> >> >> >>>>> >> before crash)
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NVE (at least 119 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> >> successfully
>> >>>>>>>>>>>>> >> >> done
>> >>>>>>>>>>>>> >> >> >>>>> >> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NVE (at least 43 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> successfully
>> >>>>>>>>>>>>> >> >> done
>> >>>>>>>>>>>>> >> >> >>>>> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> #3 no ERR writtent in mdout, ERR written in
>> >>>>>>>>>>>>> standard
>> >>>>>>>>>>>>> output
>> >>>>>>>>>>>>> >> >> >>>>> (nohup.out)
>> >>>>>>>>>>>>> >> >> >>>>> >> ----
>> >>>>>>>>>>>>> >> >> >>>>> >> cudaMemcpy GpuBuffer::Download failed
>> >>>>>>>>>>>>> unspecified
>> >>>>>>>>>>>>> launch
>> >>>>>>>>>>>>> >> >> failure
>> >>>>>>>>>>>>> >> >> >>>>> >> ----
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NPT (at least 77 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> successfully
>> >>>>>>>>>>>>> >> >> done
>> >>>>>>>>>>>>> >> >> >>>>> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NPT (at least 58 000
>> >>>>>>>>>>>>> steps
>> >>>>>>>>>>>>> successfully
>> >>>>>>>>>>>>> >> >> done
>> >>>>>>>>>>>>> >> >> >>>>> before
>> >>>>>>>>>>>>> >> >> >>>>> >> crash)
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> Dne Thu, 30 May 2013 21:27:17 +0200 Scott
>> Le
>> >>>>>>>>>>>>> Grand
>> >>>>>>>>>>>>> >> >> >>>>> >> <varelse2005.gmail.com>
>> >>>>>>>>>>>>> >> >> >>>>> >> napsal/-a:
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> Oops meant to send that to Jason...
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>> Anyway, before we all panic, we need to
>> get
>> >>>>>>>>>>>>> K20's
>> >>>>>>>>>>>>> behavior
>> >>>>>>>>>>>>> >> >> >>>>> analyzed
>> >>>>>>>>>>>>> >> >> >>>>> >>> here.
>> >>>>>>>>>>>>> >> >> >>>>> >>> If it's deterministic, this truly is a
>> >>>>>>>>>>>>> hardware
>> >>>>>>>>>>>>> issue. If
>> >>>>>>>>>>>>> >> >> not,
>> >>>>>>>>>>>>> >> >> >>>>> then
>> >>>>>>>>>>>>> >> >> >>>>> it
>> >>>>>>>>>>>>> >> >> >>>>> >>> gets interesting because 680 is
>> >>>>>>>>>>>>> deterministic as
>> >>>>>>>>>>>>> far
>> >>>>>>>>>>>>> as I
>> >>>>>>>>>>>>> >> can
>> >>>>>>>>>>>>> >> >> >>>>> tell...
>> >>>>>>>>>>>>> >> >> >>>>> >>> On May 30, 2013 12:24 PM, "Scott Le Grand"
>> >>>>>>>>>>>>> >> >> >>>>> <varelse2005.gmail.com>
>> >>>>>>>>>>>>> >> >> >>>>> >>> wrote:
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>> If the errors are not deterministically
>> >>>>>>>>>>>>> triggered,
>> >>>>>>>>>>>>> they
>> >>>>>>>>>>>>> >> >> probably
>> >>>>>>>>>>>>> >> >> >>>>> >>> won't be
>> >>>>>>>>>>>>> >> >> >>>>> >>>> fixed by the patch, alas...
>> >>>>>>>>>>>>> >> >> >>>>> >>>> On May 30, 2013 12:15 PM, "Jason Swails"
>> >>>>>>>>>>>>> >> >> >>>>> <jason.swails.gmail.com>
>> >>>>>>>>>>>>> >> >> >>>>> >>>> wrote:
>> >>>>>>>>>>>>> >> >> >>>>> >>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>> Just a reminder to everyone based on
>> what
>> >>>>>>>>>>>>> Ross
>> >>>>>>>>>>>>> said:
>> >>>>>>>>>>>>> >> there
>> >>>>>>>>>>>>> >> >> is a
>> >>>>>>>>>>>>> >> >> >>>>> >>>> pending
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> patch to pmemd.cuda that will be coming
>> out
>> >>>>>>>>>>>>> shortly
>> >>>>>>>>>>>>> >> (maybe
>> >>>>>>>>>>>>> >> >> even
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> within
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> hours). It's entirely possible that
>> >>>>>>>>>>>>> several
>> >>>>>>>>>>>>> of
>> >>>>>>>>>>>>> these
>> >>>>>>>>>>>>> > errors
>> >>>>>>>>>>>>> >> >> >>>>> are
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> fixed
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> by
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> this patch.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> All the best,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> Jason
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> On Thu, May 30, 2013 at 2:46 PM, filip
>> >>>>>>>>>>>>> fratev
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>> filipfratev.yahoo.com>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> wrote:
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > I have observed the same crashes from
>> >>>>>>>>>>>>> time
>> >>>>>>>>>>>>> to
>> >>>>>>>>>>>>> time. I
>> >>>>>>>>>>>>> > will
>> >>>>>>>>>>>>> >> >> >>>>> run
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> cellulose
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > nve for 100k and will past results
>> here.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > All the best,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > Filip
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > ______________________________******__
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > From: Scott Le Grand
>> >>>>>>>>>>>>> <varelse2005.gmail.com>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > To: AMBER Mailing List
>> >>>>>>>>>>>>> <amber.ambermd.org>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > Sent: Thursday, May 30, 2013 9:01 PM
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > Subject: Re: [AMBER] experiences with
>> >>>>>>>>>>>>> EVGA
>> >>>>>>>>>>>>> GTX
>> >>>>>>>>>>>>> TITAN
>> >>>>>>>>>>>>> >> >> >>>>> Superclocked
>> >>>>>>>>>>>>> >> >> >>>>> -
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > memtestG80 - UNDERclocking in Linux ?
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > Run cellulose nve for 100k iterations
>> >>>>>>>>>>>>> twice
>> >>>>>>>>>>>>> . If
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> final
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> energies
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> don't
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > match, you have a hardware issue. No
>> >>>>>>>>>>>>> need
>> >>>>>>>>>>>>> to
>> >>>>>>>>>>>>> play
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> >> >> ntpr
>> >>>>>>>>>>>>> >> >> >>>>> or
>> >>>>>>>>>>>>> >> >> >>>>> any
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> other
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > variable.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > On May 30, 2013 10:58 AM,
>> >>>>>>>>>>>>> <pavel.banas.upol.cz>
>> >>>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Dear all,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > I would also like to share one of my
>> >>>>>>>>>>>>> experience
>> >>>>>>>>>>>>> with
>> >>>>>>>>>>>>> >> >> titan
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> cards. We
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> have
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > one gtx titan card and with one
>> system
>> >>>>>>>>>>>>> (~55k
>> >>>>>>>>>>>>> atoms,
>> >>>>>>>>>>>>> > NVT,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> RNA+waters)
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> we
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > run
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > into same troubles you are
>> describing.
>> >>>>>>>>>>>>> I
>> >>>>>>>>>>>>> was
>> >>>>>>>>>>>>> also
>> >>>>>>>>>>>>> >> >> playing
>> >>>>>>>>>>>>> >> >> >>>>> with
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> ntpr
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> to
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > figure out what is going on, step by
>> >>>>>>>>>>>>> step.
>> >>>>>>>>>>>>> I
>> >>>>>>>>>>>>> >> understand
>> >>>>>>>>>>>>> >> >> >>>>> that
>> >>>>>>>>>>>>> >> >> >>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> code
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> is
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > using different routines for
>> >>>>>>>>>>>>> calculation
>> >>>>>>>>>>>>> >> >> energies+forces or
>> >>>>>>>>>>>>> >> >> >>>>> only
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> forces.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > The
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > simulations of other systems are
>> >>>>>>>>>>>>> perfectly
>> >>>>>>>>>>>>> stable,
>> >>>>>>>>>>>>> >> >> running
>> >>>>>>>>>>>>> >> >> >>>>> for
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> days
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> and
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > weeks. Only that particular system
>> >>>>>>>>>>>>> systematically
>> >>>>>>>>>>>>> >> ends
>> >>>>>>>>>>>>> >> >> up
>> >>>>>>>>>>>>> >> >> >>>>> with
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> this
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > error.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > However, there was one interesting
>> >>>>>>>>>>>>> issue.
>> >>>>>>>>>>>>> When
>> >>>>>>>>>>>>> I
>> >>>>>>>>>>>>> set
>> >>>>>>>>>>>>> >> >> >>>>> ntpr=1,
>> >>>>>>>>>>>>> >> >> >>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> error
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > vanished (systematically in multiple
>> >>>>>>>>>>>>> runs)
>> >>>>>>>>>>>>> and
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> simulation
>> >>>>>>>>>>>>> >> >> >>>>> was
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> able to
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > run for more than millions of steps
>> (I
>> >>>>>>>>>>>>> was
>> >>>>>>>>>>>>> not
>> >>>>>>>>>>>>> let
>> >>>>>>>>>>>>> it
>> >>>>>>>>>>>>> >> >> >>>>> running
>> >>>>>>>>>>>>> >> >> >>>>> for
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> weeks
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > as
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > in the meantime I shifted that
>> >>>>>>>>>>>>> simulation
>> >>>>>>>>>>>>> to
>> >>>>>>>>>>>>> other
>> >>>>>>>>>>>>> >> card
>> >>>>>>>>>>>>> >> >> -
>> >>>>>>>>>>>>> >> >> >>>>> need
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> data,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> not
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > testing). All other setting of ntpr
>> >>>>>>>>>>>>> failed.
>> >>>>>>>>>>>>> As
>> >>>>>>>>>>>>> I
>> >>>>>>>>>>>>> read
>> >>>>>>>>>>>>> >> >> this
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> discussion, I
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > tried to set ene_avg_sampling=1 with
>> >>>>>>>>>>>>> some
>> >>>>>>>>>>>>> high
>> >>>>>>>>>>>>> value
>> >>>>>>>>>>>>> >> of
>> >>>>>>>>>>>>> >> >> >>>>> ntpr
>> >>>>>>>>>>>>> >> >> >>>>> (I
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> expected
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > that this will shift the code to
>> >>>>>>>>>>>>> permanently
>> >>>>>>>>>>>>> use
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> force+energies
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> part
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > of
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > the code, similarly to ntpr=1), but
>> the
>> >>>>>>>>>>>>> error
>> >>>>>>>>>>>>> >> occurred
>> >>>>>>>>>>>>> >> >> >>>>> again.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > I know it is not very conclusive for
>> >>>>>>>>>>>>> finding
>> >>>>>>>>>>>>> out
>> >>>>>>>>>>>>> what
>> >>>>>>>>>>>>> > is
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> happening,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> at
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > least
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > not for me. Do you have any idea,
>> why
>> >>>>>>>>>>>>> ntpr=1
>> >>>>>>>>>>>>> might
>> >>>>>>>>>>>>> > help?
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > best regards,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Pavel
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > --
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Pavel Banáš
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > pavel.banas.upol.cz
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Department of Physical Chemistry,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Palacky University Olomouc
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Czech Republic
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > ---------- Původní zpráva ----------
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Od: Jason Swails
>> >>>>>>>>>>>>> <jason.swails.gmail.com>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Datum: 29. 5. 2013
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Předmět: Re: [AMBER] experiences
>> with
>> >>>>>>>>>>>>> EVGA
>> >>>>>>>>>>>>> GTX
>> >>>>>>>>>>>>> TITAN
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> Superclocked -
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > memtestG
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > 80 - UNDERclocking in Linux ?
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > "I'll answer a little bit:
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > NTPR=10 Etot after 2000 steps
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443256.6711
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443256.6711
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > > NTPR=200 Etot after 2000 steps
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443261.0705
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443261.0705
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > > Any idea why energies should
>> depend
>> >>>>>>>>>>>>> on
>> >>>>>>>>>>>>> frequency
>> >>>>>>>>>>>>> of
>> >>>>>>>>>>>>> >> >> >>>>> energy
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> records
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > (NTPR)
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > ?
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > It is a subtle point, but the
>> answer is
>> >>>>>>>>>>>>> 'different
>> >>>>>>>>>>>>> >> code
>> >>>>>>>>>>>>> >> >> >>>>> paths.'
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> In
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > general, it is NEVER necessary to
>> >>>>>>>>>>>>> compute
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> actual
>> >>>>>>>>>>>>> >> >> energy
>> >>>>>>>>>>>>> >> >> >>>>> of a
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> molecule
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > during the course of standard
>> molecular
>> >>>>>>>>>>>>> dynamics
>> >>>>>>>>>>>>> (by
>> >>>>>>>>>>>>> >> >> >>>>> analogy, it
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> is
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> NEVER
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > necessary to compute atomic forces
>> >>>>>>>>>>>>> during
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> course
>> >>>>>>>>>>>>> >> of
>> >>>>>>>>>>>>> >> >> >>>>> random
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> Monte
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > Carlo
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > sampling).
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > For performance's sake, then,
>> >>>>>>>>>>>>> pmemd.cuda
>> >>>>>>>>>>>>> computes
>> >>>>>>>>>>>>> >> only
>> >>>>>>>>>>>>> >> >> the
>> >>>>>>>>>>>>> >> >> >>>>> force
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> when
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > energies are not requested, leading
>> to
>> >>>>>>>>>>>>> a
>> >>>>>>>>>>>>> different
>> >>>>>>>>>>>>> >> >> order of
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> operations
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > for
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > those runs. This difference
>> ultimately
>> >>>>>>>>>>>>> causes
>> >>>>>>>>>>>>> >> >> divergence.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > To test this, try setting the
>> variable
>> >>>>>>>>>>>>> >> >> ene_avg_sampling=10
>> >>>>>>>>>>>>> >> >> >>>>> in
>> >>>>>>>>>>>>> >> >> >>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> &cntrl
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > section. This will force pmemd.cuda
>> to
>> >>>>>>>>>>>>> compute
>> >>>>>>>>>>>>> >> energies
>> >>>>>>>>>>>>> >> >> >>>>> every 10
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> steps
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > (for energy averaging), which will
>> in
>> >>>>>>>>>>>>> turn
>> >>>>>>>>>>>>> make
>> >>>>>>>>>>>>> the
>> >>>>>>>>>>>>> >> >> >>>>> followed
>> >>>>>>>>>>>>> >> >> >>>>> code
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> path
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > identical for any multiple-of-10
>> value
>> >>>>>>>>>>>>> of
>> >>>>>>>>>>>>> ntpr.
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > --
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Jason M. Swails
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Quantum Theory Project,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > University of Florida
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > Ph.D. Candidate
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > 352-392-4032
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > ______________________________****
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> >>>>>>>>>>>>> mailman/listinfo/amber<http://**
>> lists.ambermd.org/**mailman/**
>> >>>>>>>>>>>>> listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> "
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > ______________________________****
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> >>>>>>>>>>>>> mailman/listinfo/amber<http://**
>> lists.ambermd.org/**mailman/**
>> >>>>>>>>>>>>> listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > ______________________________****
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> >>>>>>>>>>>>> mailman/listinfo/amber<http://**
>> lists.ambermd.org/**mailman/**
>> >>>>>>>>>>>>> listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > ______________________________****
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> >>>>>>>>>>>>> mailman/listinfo/amber<http://**
>> lists.ambermd.org/**mailman/**
>> >>>>>>>>>>>>> listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> --
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> Jason M. Swails
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> Quantum Theory Project,
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> University of Florida
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> Ph.D. Candidate
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> 352-392-4032
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> ______________________________****
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> >>>>>>>>>>>>> mailman/listinfo/amber<http://**
>> lists.ambermd.org/**mailman/**
>> >>>>>>>>>>>>> listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>> ______________________________****
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >>> AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >>> AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/******mailman/listinfo/amber<
>> http://lists.ambermd.org/****mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/**mailman/**listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>> __________ Informace od ESET NOD32
>> Antivirus,
>> >>>>>>>>>>>>> verze
>> >>>>>>>>>>>>> >> databaze
>> >>>>>>>>>>>>> >> >> 8394
>> >>>>>>>>>>>>> >> >> >>>>> >>> (20130530) __________
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>> http://www.eset.cz
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >> --
>> >>>>>>>>>>>>> >> >> >>>>> >> Tato zpráva byla vytvořena převratným
>> >>>>>>>>>>>>> poštovním
>> >>>>>>>>>>>>> klientem
>> >>>>>>>>>>>>> > Opery:
>> >>>>>>>>>>>>> >> >> >>>>> >> http://www.opera.com/mail/
>> >>>>>>>>>>>>> >> >> >>>>> >> ______________________________**
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> >> AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> >> AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> >>
>> >>>>>>>>>>>>> >> >> >>>>> > ______________________________**
>> >>>>>>>>>>>>> **_________________
>> >>>>>>>>>>>>> >> >> >>>>> > AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> > AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> > __________ Informace od ESET NOD32
>> Antivirus,
>> >>>>>>>>>>>>> verze
>> >>>>>>>>>>>>> databaze
>> >>>>>>>>>>>>> >> >> 8394
>> >>>>>>>>>>>>> >> >> >>>>> > (20130530) __________
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> > http://www.eset.cz
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>> >
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>> --
>> >>>>>>>>>>>>> >> >> >>>>> Tato zpráva byla vytvořena převratným
>> poštovním
>> >>>>>>>>>>>>> klientem
>> >>>>>>>>>>>>> Opery:
>> >>>>>>>>>>>>> >> >> >>>>> http://www.opera.com/mail/
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> ______________________________****_________________
>> >>>>>>>>>>>>> >> >> >>>>> AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>>>> AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>>>> >> >> >>>
>> ______________________________****_________________
>> >>>>>>>>>>>>> >> >> >>> AMBER mailing list
>> >>>>>>>>>>>>> >> >> >>> AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>> __________ Informace od ESET NOD32 Antivirus,
>> verze
>> >>>>>>>>>>>>> databaze
>> >>>>>>>>>>>>> 8395
>> >>>>>>>>>>>>> >> >> >>> (20130531) __________
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>> http://www.eset.cz
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >>
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> --
>> >>>>>>>>>>>>> >> >> Tato zpráva byla vytvořena převratným poštovním
>> >>>>>>>>>>>>> klientem
>> >>>>>>>>>>>>> Opery:
>> >>>>>>>>>>>>> >> >> http://www.opera.com/mail/
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >> ______________________________****_________________
>> >>>>>>>>>>>>> >> >> AMBER mailing list
>> >>>>>>>>>>>>> >> >> AMBER.ambermd.org
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> >>
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > __________ Informace od ESET NOD32 Antivirus, verze
>> >>>>>>>>>>>>> databaze
>> >>>>>>>>>>>>> 8397
>> >>>>>>>>>>>>> >> > (20130531) __________
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz - poskozeny archiv
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> GB_out_plus_diff_Files.tar
>> >>>>>>>>>>>>> >> > - poskozeny archiv
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> GB_out_plus_diff_Files.tar.gz -
>> >>>>>>>>>>>>> >> > poskozeny archiv
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> GB_out_plus_diff_Files.tar.gz >
>> >>>>>>>>>>>>> >> GZIP
>> >>>>>>>>>>>>> >> > > GB_out_plus_diff_Files.tar - poskozeny archiv
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> GB_out_plus_diff_Files.tar.gz >
>> >>>>>>>>>>>>> >> GZIP
>> >>>>>>>>>>>>> >> > > GB_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> GB_nucleosome-sim3.mdout-full -
>> >>>>>>>>>>>>> >> > vyskytl se problem pri cteni archivu
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz - poskozeny archiv
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar - poskozeny archiv
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> PME_out_plus_diff_Files.tar.gz -
>> >>>>>>>>>>>>> >> > poskozeny archiv
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> PME_out_plus_diff_Files.tar.gz >
>> >>>>>>>>>>>>> >> > GZIP > PME_out_plus_diff_Files.tar - poskozeny archiv
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> >>>>>>>>>>>>> >> > PME_out_plus_diff_Filestar > TAR >
>> >>>>>>>>>>>>> PME_out_plus_diff_Files.tar.gz
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >> GZIP
>> >>>>>>>>>>>>> >> > > PME_out_plus_diff_Files.tar > TAR >
>> >>>>>>>>>>>>> >> > PME_JAC_production_NPT-sim3.****mdout-full - vyskytl
>> se
>> >>>>>>>>>>>>> problem
>> >>>>>>>>>>>>> pri
>> >>>>>>>>>>>>> cteni
>> >>>>>>>>>>>>> >> > archivu
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >> > http://www.eset.cz
>> >>>>>>>>>>>>> >> >
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> --
>> >>>>>>>>>>>>> >> Tato zpráva byla vytvořena převratným poštovním
>> klientem
>> >>>>>>>>>>>>> Opery:
>> >>>>>>>>>>>>> >> http://www.opera.com/mail/
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> >> ______________________________****_________________
>> >>>>>>>>>>>>> >> AMBER mailing list
>> >>>>>>>>>>>>> >> AMBER.ambermd.org
>> >>>>>>>>>>>>> >>
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> > ______________________________****_________________
>> >>>>>>>>>>>>> > AMBER mailing list
>> >>>>>>>>>>>>> > AMBER.ambermd.org
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> > __________ Informace od ESET NOD32 Antivirus, verze
>> >>>>>>>>>>>>> databaze
>> >>>>>>>>>>>>> 8398
>> >>>>>>>>>>>>> > (20130531) __________
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> > http://www.eset.cz
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> --
>> >>>>>>>>>>>>> Tato zpráva byla vytvořena převratným poštovním klientem
>> >>>>>>>>>>>>> Opery:
>> >>>>>>>>>>>>> http://www.opera.com/mail/
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> ______________________________****_________________
>> >>>>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>>>>> >
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> __________ Informace od ESET NOD32 Antivirus, verze databaze
>> >>>>>>>>>>> 8401
>> >>>>>>>>>>> (20130601) __________
>> >>>>>>>>>>>
>> >>>>>>>>>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>>>>>>
>> >>>>>>>>>>> http://www.eset.cz
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>> --
>> >>>>>>>>> Tato zpráva byla vytvořena převratným poštovním klientem
>> Opery:
>> >>>>>>>>> http://www.opera.com/mail/
>> >>>>>>>>>
>> >>>>>>>>> ______________________________**_________________
>> >>>>>>>>> AMBER mailing list
>> >>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>
>> >>>>>>> ______________________________**_________________
>> >>>>>> AMBER mailing list
>> >>>>>> AMBER.ambermd.org
>> >>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>>>>>
>> >>>>>> __________ Informace od ESET NOD32 Antivirus, verze databaze 8403
>> >>>>>> (20130602) __________
>> >>>>>>
>> >>>>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>>>>
>> >>>>>> http://www.eset.cz
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >>
>> >> --
>> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> >> http://www.opera.com/mail/
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> http://www.opera.com/mail/
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 11:00:03 PDT
